In case anyone was interested, here is everything I needed to get working and rooted. (The links below are to my mirror, feel free to gather them elsewhere. I found gathering all this to be a royal pita, but I don't do much/anything with Windows, so ymmv.)

You probably won't lose your data, but don't be careless. Take a backup first, remove your external SD card, etc.

This should work no matter what mod you have running currently.

Download some stuff:
Odin Tar
Odin program
Samsung Drivers
Modded Philz Recovery
Superuser.zip (The closed-source one, unfortunately supersu didn't work for me.)

Install the drivers, unzip the Odin Tar zip (so you have a tar.md5) and flash that from download mode. (Boot holding vol-down and home.)
Let the phone reboot on it's own, it will boot recovery to update the bootloader/modem/etc and then boot Android.
Once it is in Android, go back to download mode and flash the modded recovery. Then boot recovery mode (vol-up and home) and flash (or sideload) the superuser.zip.

Once you reboot from there, you should be up to date and rooted. This WILL WILL WILL set the warranty flag. If you stop with the first time you boot into Android, it shouldn't change the flag (if it is unset, it should stay that way.)

And for pete's sake, if it helped hit thanks. Costs nothing